Automated design of genomic Southern blot probes

Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant

Design Case - ProbeDesign53 - back to list

Summary

./analyse_probe_search_results : Mon Sep 26 11:57:28 2005

Connected to host: host, as user: user
Database       : southern_blot_designs

Fetched probe design: ProbeDesign53
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : X
  id            : 38
  strand        : 1
  -------------

Design window length: 6001bp

All jobs for probe design are successful - total: 108
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 2146 putative probes to analyse

Selection criteria to rank probes:
  Minimum score ratio             : 10
  (i.e. self-hit must score at least 10 times higher than the next best hit)
  Maximum percent repetitive bases: 5
  Favour probes to the 3prime end of design window
  ------------------------

Putative probes without hits                : 0
Putative probes with single_self_hit        : 2146/2146
Putative probes exceeding selection criteria: 55/2146

PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW
--------------------------------------------------------------

Image

Unique (yellow), passed (green) and failed putative probes in the design window

Chart

Unique putative probes

No probes

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
4129670018.63500-332518.6
4129770018.63500-336018.6
4145765017.33250-332817.3
4145865017.33250-336017.3
4145965017.33250-339217.3
4114975019.937501.5333017.0
4163160016.03000-330016.0
4163260016.03000-333016.0
4163360016.03000-336016.0
4163460016.03000-339016.0
4163560016.03000-342016.0
4163660016.03000-345016.0
4146065017.332500.8342415.7
4182555014.62750-332114.6
4182655014.62750-334814.6
4182755014.62750-337514.6
4182855014.62750-340214.6
4182955014.62750-342914.6
4183055014.62750-345614.6
4183155014.62750-348314.6
4183255014.62750-351014.6
4203650013.32500-330013.3
4203750013.32500-332513.3
4203850013.32500-335013.3
4203950013.32500-337513.3
4204050013.32500-340013.3
4204150013.32500-342513.3
4204250013.32500-345013.3
4204350013.32500-347513.3
4204450013.32500-350013.3
4204550013.32500-352513.3
4204650013.32500-355013.3
4092685012.54250-508212.5
4105580011.84000-508011.8
4105680011.84000-512011.8
4129870018.635003.7339511.2
4119675011.03750-506911.0
4119775011.03750-510611.0
4119875011.03750-514311.0
4119975011.03750-518011.0
4204750013.325001.2357510.9
4080390010.34500-504010.3
4134670010.33500-507510.3
4134770010.33500-511010.3
4134870010.33500-514510.3
4134970010.33500-518010.3
4135070010.33500-521510.3
4135170010.335001.052508.3
4183355014.627503.335378.1
4105780011.840002.151607.5
4092785012.542503.651245.2
4120075011.037503.252174.6
4080490013.245004.750853.9
4069095010.147503.850292.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
4163760016.030001.8348012.3

Overall score = score_ratio - 2 * repetitive DNA content

© G2C 2014. The Genes to Cognition Programme received funding from The Wellcome Trust and the EU FP7 Framework Programmes:
EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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